X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details 100 mM MES, 40 mM MgOAc, 15% 2-methyl-2,4-pentanediol (MPD), 10 mM EDTA, pH 7.0, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 136.02 α = 90
b = 300.38 β = 113.73
c = 145.81 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 31-ID -- APS 31-ID

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.78 50 97.2 0.123 -- -- 3.7 -- 257519 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.78 2.9 85.7 0.442 -- -- 3.3 22640

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.78 48.68 -- 0.0 -- 256472 5191 95.84 -- 0.218 0.217 0.259 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.78 2.852 -- 306 13929 0.314 0.417 -- 72.11
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 58.954
Anisotropic B[1][1] 0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.03
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 37.481
r_chiral_restr 0.077
r_nbtor_refined 0.302
r_symmetry_vdw_refined 0.23
r_angle_refined_deg 1.14
r_xyhbond_nbd_refined 0.137
r_nbd_refined 0.207
r_symmetry_hbond_refined 0.171
r_dihedral_angle_3_deg 18.038
r_mcangle_it 1.762
r_bond_refined_d 0.008
r_dihedral_angle_4_deg 15.853
r_gen_planes_refined 0.003
r_mcbond_it 1.043
r_dihedral_angle_1_deg 5.791
r_scbond_it 0.489
r_scangle_it 0.777
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 49298
Nucleic Acid Atoms 0
Heterogen Atoms 122
Solvent Atoms 4

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.2.0005
PDB_EXTRACT data extraction version: 3.100